Merge branch 'master' into enh/NewDipyInterfaces

Conflicts:
	CHANGES

Author: oesteban

CHANGES

@@ -3,6 +3,8 @@ Next release
 
 * ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
        (https://github.com/nipy/nipype/pull/1090)
+* FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089,
+       replaced by https://github.com/nipy/nipype/pull/1093)
 * ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings
        (https://github.com/nipy/nipype/pull/1016)
 * FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,
@@ -53,6 +55,7 @@ Next release
 * ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
 * FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083)
 * FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)
+* FIX: Add QA output for TSNR to resting workflow (https://github.com/nipy/nipype/pull/1088)
 
 Release 0.10.0 (October 10, 2014)
 ============

examples/rsfmri_vol_surface_preprocessing_nipy.py

@@ -387,7 +387,8 @@ def create_reg_workflow(name='registration'):
                                                           'transformed_mean',
                                                           'segmentation_files',
                                                           'anat2target',
-                                                          'aparc'
+                                                          'aparc',
+                                                          'min_cost_file'
                                                           ]),
                       name='outputspec')
 
@@ -505,7 +506,7 @@ def create_reg_workflow(name='registration'):
     reg.inputs.args = '--float'
     reg.inputs.output_warped_image = 'output_warped_image.nii.gz'
     reg.inputs.num_threads = 4
-    reg.plugin_args = {'qsub_args': '-l nodes=1:ppn=4'}
+    reg.plugin_args = {'sbatch_args': '-c%d' % 4}
     register.connect(stripper, 'out_file', reg, 'moving_image')
     register.connect(inputnode,'target_image', reg,'fixed_image')
 
@@ -531,6 +532,7 @@ def create_reg_workflow(name='registration'):
     warpmean.inputs.terminal_output = 'file'
     warpmean.inputs.args = '--float'
     warpmean.inputs.num_threads = 4
+    warpmean.plugin_args = {'sbatch_args': '-c%d' % 4}
 
     register.connect(inputnode,'target_image', warpmean,'reference_image')
     register.connect(inputnode, 'mean_image', warpmean, 'input_image')
@@ -554,6 +556,8 @@ def create_reg_workflow(name='registration'):
     register.connect(reg, 'composite_transform',
                      outputnode, 'anat2target_transform')
     register.connect(merge, 'out', outputnode, 'transforms')
+    register.connect(bbregister, 'min_cost_file',
+                     outputnode, 'min_cost_file')
 
     return register
 
@@ -593,6 +597,7 @@ def create_workflow(files,
     realign.inputs.slice_times = slice_times
     realign.inputs.tr = TR
     realign.inputs.slice_info = 2
+    realign.plugin_args = {'sbatch_args': '-c%d' % 4}
 
 
     # Comute TSNR on realigned data regressing polynomials upto order 2
@@ -615,6 +620,13 @@ def create_workflow(files,
     registration.inputs.inputspec.subjects_dir = subjects_dir
     registration.inputs.inputspec.target_image = target_file
 
+    """Quantify TSNR in each freesurfer ROI
+    """
+    get_roi_tsnr = MapNode(fs.SegStats(default_color_table=True),
+                           iterfield=['in_file'], name='get_aparc_tsnr')
+    get_roi_tsnr.inputs.avgwf_txt_file = True
+    wf.connect(tsnr, 'tsnr_file', get_roi_tsnr, 'in_file')
+    wf.connect(registration, 'outputspec.aparc', get_roi_tsnr, 'segmentation_file')
 
     """Use :class:`nipype.algorithms.rapidart` to determine which of the
     images in the functional series are outliers based on deviations in
@@ -754,7 +766,8 @@ def merge_files(in1, in2):
     warpall.inputs.terminal_output = 'file'
     warpall.inputs.reference_image = target_file
     warpall.inputs.args = '--float'
-    warpall.inputs.num_threads = 1
+    warpall.inputs.num_threads = 2
+    warpall.plugin_args = {'sbatch_args': '-c%d' % 2}
 
     # transform to target
     wf.connect(collector, 'out', warpall, 'input_image')
@@ -874,13 +887,14 @@ def get_names(files, suffix):
     substitutions += [("_filtermotion%d" % i,"") for i in range(11)[::-1]]
     substitutions += [("_filter_noise_nosmooth%d" % i,"") for i in range(11)[::-1]]
     substitutions += [("_makecompcorfilter%d" % i,"") for i in range(11)[::-1]]
+    substitutions += [("_get_aparc_tsnr%d/" % i, "run%d_" % (i + 1)) for i in range(11)[::-1]]
 
-    substitutions += [("T1_out_brain_pve_0_maths_warped","compcor_csf"),
-                      ("T1_out_brain_pve_1_maths_warped","compcor_gm"),
+    substitutions += [("T1_out_brain_pve_0_maths_warped", "compcor_csf"),
+                      ("T1_out_brain_pve_1_maths_warped", "compcor_gm"),
                       ("T1_out_brain_pve_2_maths_warped", "compcor_wm"),
-                      ("output_warped_image_maths","target_brain_mask"),
-                      ("median_brain_mask","native_brain_mask"),
-                      ("corr_","")]
+                      ("output_warped_image_maths", "target_brain_mask"),
+                      ("median_brain_mask", "native_brain_mask"),
+                      ("corr_", "")]
 
     regex_subs = [('_combiner.*/sar', '/smooth/'),
                   ('_combiner.*/ar', '/unsmooth/'),
@@ -910,6 +924,11 @@ def get_names(files, suffix):
     wf.connect(filter1, 'out_pf', datasink, 'resting.qa.compmaps.@mc_pF')
     wf.connect(filter2, 'out_f', datasink, 'resting.qa.compmaps')
     wf.connect(filter2, 'out_pf', datasink, 'resting.qa.compmaps.@p')
+    wf.connect(registration, 'outputspec.min_cost_file', datasink, 'resting.qa.mincost')
+    wf.connect(tsnr, 'tsnr_file', datasink, 'resting.qa.tsnr.@map')
+    wf.connect([(get_roi_tsnr, datasink, [('avgwf_txt_file', 'resting.qa.tsnr'),
+                                          ('summary_file', 'resting.qa.tsnr.@summary')])])
+
     wf.connect(bandpass, 'out_files', datasink, 'resting.timeseries.@bandpassed')
     wf.connect(smooth, 'out_file', datasink, 'resting.timeseries.@smoothed')
     wf.connect(createfilter1, 'out_files',

nipype/interfaces/dcmstack.py

@@ -1,4 +1,4 @@
-"""Provides interfaces to various commands provided by FreeSurfer
+"""Provides interfaces to various commands provided by dcmstack
 
    Change directory to provide relative paths for doctests
    >>> import os
@@ -9,8 +9,10 @@
 """
 
 from __future__ import absolute_import
-import os, string
-from os import path
+import os
+import string
+import errno
+from os import path as op
 from glob import glob
 from nipype.interfaces.base import (TraitedSpec,
                                     DynamicTraitedSpec,
@@ -33,6 +35,7 @@
 except ImportError:
     have_dcmstack = False
 
+
 def sanitize_path_comp(path_comp):
     result = []
     for char in path_comp:
@@ -42,16 +45,18 @@ def sanitize_path_comp(path_comp):
             result.append(char)
     return ''.join(result)
 
+
 class NiftiGeneratorBaseInputSpec(TraitedSpec):
     out_format = traits.Str(desc="String which can be formatted with "
                             "meta data to create the output filename(s)")
-    out_ext = traits.Str('.nii.gz',
-                         usedefault=True,
+    out_ext = traits.Str('.nii.gz', usedefault=True,
                          desc="Determines output file type")
+    out_path = Directory(desc='output path, current working directory if not set')
+
 
 class NiftiGeneratorBase(BaseInterface):
     '''Base class for interfaces that produce Nifti files, potentially with
-    embeded meta data.'''
+    embedded meta data.'''
     def _get_out_path(self, meta, idx=None):
         '''Return the output path for the gernerated Nifti.'''
         if self.inputs.out_format:
@@ -73,7 +78,22 @@ def _get_out_path(self, meta, idx=None):
             out_fmt = '-'.join(out_fmt)
         out_fn = (out_fmt % meta) + self.inputs.out_ext
         out_fn = sanitize_path_comp(out_fn)
-        return path.join(os.getcwd(), out_fn)
+
+        out_path = os.getcwd()
+        if isdefined(self.inputs.out_path):
+            out_path = op.abspath(self.inputs.out_path)
+
+            # now, mkdir -p $out_path
+            try:
+                os.makedirs(out_path)
+            except OSError as exc:  # Python >2.5
+                if exc.errno == errno.EEXIST and op.isdir(out_path):
+                    pass
+                else:
+                    raise
+
+        return op.join(out_path, out_fn)
+
 
 class DcmStackInputSpec(NiftiGeneratorBaseInputSpec):
     dicom_files = traits.Either(InputMultiPath(File(exists=True)),
@@ -92,6 +112,7 @@ class DcmStackInputSpec(NiftiGeneratorBaseInputSpec):
 class DcmStackOutputSpec(TraitedSpec):
     out_file = File(exists=True)
 
+
 class DcmStack(NiftiGeneratorBase):
     '''Create one Nifti file from a set of DICOM files. Can optionally embed
     meta data.
@@ -111,8 +132,8 @@ class DcmStack(NiftiGeneratorBase):
 
     def _get_filelist(self, trait_input):
         if isinstance(trait_input, six.string_types):
-            if path.isdir(trait_input):
-                return glob(path.join(trait_input, '*.dcm'))
+            if op.isdir(trait_input):
+                return glob(op.join(trait_input, '*.dcm'))
             else:
                 return glob(trait_input)
 
@@ -147,9 +168,11 @@ def _list_outputs(self):
         outputs["out_file"] = self.out_path
         return outputs
 
+
 class GroupAndStackOutputSpec(TraitedSpec):
     out_list = traits.List(desc="List of output nifti files")
 
+
 class GroupAndStack(DcmStack):
     '''Create (potentially) multiple Nifti files for a set of DICOM files.
     '''
@@ -177,6 +200,7 @@ def _list_outputs(self):
         outputs["out_list"] = self.out_list
         return outputs
 
+
 class LookupMetaInputSpec(TraitedSpec):
     in_file = File(mandatory=True,
                    exists=True,
@@ -189,8 +213,9 @@ class LookupMetaInputSpec(TraitedSpec):
                               "lookup and the values specify the output names")
                              )
 
+
 class LookupMeta(BaseInterface):
-    '''Lookup meta data values from a Nifti with embeded meta data.
+    '''Lookup meta data values from a Nifti with embedded meta data.
 
     Example
     -------
@@ -225,13 +250,13 @@ def _outputs(self):
             outputs.add_trait(out_name, traits.Any)
             undefined_traits[out_name] = Undefined
         outputs.trait_set(trait_change_notify=False, **undefined_traits)
-        #Not sure why this is needed
+        # Not sure why this is needed
         for out_name in self._meta_keys.values():
             _ = getattr(outputs, out_name)
         return outputs
 
     def _run_interface(self, runtime):
-        #If the 'meta_keys' input is a list, covert it to a dict
+        # If the 'meta_keys' input is a list, covert it to a dict
         self._make_name_map()
         nw = NiftiWrapper.from_filename(self.inputs.in_file)
         self.result = {}
@@ -245,6 +270,7 @@ def _list_outputs(self):
         outputs.update(self.result)
         return outputs
 
+
 class CopyMetaInputSpec(TraitedSpec):
     src_file = File(mandatory=True, exists=True)
     dest_file = File(mandatory=True, exists=True)
@@ -254,9 +280,11 @@ class CopyMetaInputSpec(TraitedSpec):
     exclude_classes = traits.List(desc="List of meta data "
                                   "classifications to exclude")
 
+
 class CopyMetaOutputSpec(TraitedSpec):
     dest_file = File(exists=True)
 
+
 class CopyMeta(BaseInterface):
     '''Copy meta data from one Nifti file to another. Useful for preserving
     meta data after some processing steps.'''
@@ -288,8 +316,8 @@ def _run_interface(self, runtime):
         dest.meta_ext.slice_dim = src.meta_ext.slice_dim
         dest.meta_ext.shape = src.meta_ext.shape
 
-        self.out_path = path.join(os.getcwd(),
-                                  path.basename(self.inputs.dest_file))
+        self.out_path = op.join(os.getcwd(),
+                                  op.basename(self.inputs.dest_file))
         dest.to_filename(self.out_path)
 
         return runtime
@@ -299,6 +327,7 @@ def _list_outputs(self):
         outputs['dest_file'] = self.out_path
         return outputs
 
+
 class MergeNiftiInputSpec(NiftiGeneratorBaseInputSpec):
     in_files = traits.List(mandatory=True,
                            desc="List of Nifti files to merge")
@@ -310,16 +339,19 @@ class MergeNiftiInputSpec(NiftiGeneratorBaseInputSpec):
                            "specified, the last singular or "
                            "non-existant dimension is used.")
 
+
 class MergeNiftiOutputSpec(TraitedSpec):
     out_file = File(exists=True, desc="Merged Nifti file")
 
+
 def make_key_func(meta_keys, index=None):
     def key_func(src_nii):
         result = [src_nii.get_meta(key, index) for key in meta_keys]
         return result
 
     return key_func
 
+
 class MergeNifti(NiftiGeneratorBase):
     '''Merge multiple Nifti files into one. Merges together meta data
     extensions as well.'''
@@ -353,18 +385,23 @@ def _list_outputs(self):
         outputs['out_file'] = self.out_path
         return outputs
 
+
 class SplitNiftiInputSpec(NiftiGeneratorBaseInputSpec):
     in_file = File(exists=True, mandatory=True, desc="Nifti file to split")
     split_dim = traits.Int(desc="Dimension to split along. If not "
                            "specified, the last dimension is used.")
 
+
 class SplitNiftiOutputSpec(TraitedSpec):
     out_list = traits.List(File(exists=True),
                            desc="Split Nifti files")
 
+
 class SplitNifti(NiftiGeneratorBase):
-    '''Split one Nifti file into many along the specified dimension. Each
-    result has an updated meta data extension as well.'''
+    '''
+    Split one Nifti file into many along the specified dimension. Each
+    result has an updated meta data extension as well.
+    '''
     input_spec = SplitNiftiInputSpec
     output_spec = SplitNiftiOutputSpec
 

nipype/interfaces/io.py

@@ -1951,7 +1951,7 @@ def _list_outputs(self):
         if not isdefined(self.inputs.out_file):
             out_file = op.abspath('datasink.json')
         else:
-            out_file = self.inputs.out_file
+            out_file = op.abspath(self.inputs.out_file)
 
         out_dict = self.inputs.in_dict
 

nipype/interfaces/tests/test_auto_DcmStack.py

@@ -13,6 +13,7 @@ def test_DcmStack_inputs():
     out_ext=dict(usedefault=True,
     ),
     out_format=dict(),
+    out_path=dict(),
     )
     inputs = DcmStack.input_spec()
 

nipype/interfaces/tests/test_auto_GroupAndStack.py

@@ -13,6 +13,7 @@ def test_GroupAndStack_inputs():
     out_ext=dict(usedefault=True,
     ),
     out_format=dict(),
+    out_path=dict(),
     )
     inputs = GroupAndStack.input_spec()
 

nipype/interfaces/tests/test_auto_MergeNifti.py

@@ -9,6 +9,7 @@ def test_MergeNifti_inputs():
     out_ext=dict(usedefault=True,
     ),
     out_format=dict(),
+    out_path=dict(),
     sort_order=dict(),
     )
     inputs = MergeNifti.input_spec()

nipype/interfaces/tests/test_auto_SplitNifti.py

@@ -8,6 +8,7 @@ def test_SplitNifti_inputs():
     out_ext=dict(usedefault=True,
     ),
     out_format=dict(),
+    out_path=dict(),
     split_dim=dict(),
     )
     inputs = SplitNifti.input_spec()